HC
Hamidreza Chitsaz
cs.LGq-bio.BMq-bio.GNAlgorithmscs.CEcs.RObioinformaticsclustering generaDeep LearningDNA methylation
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
35 papers in the corpus · 2009–2024Aryana-bs: context-aware alignment of bisulfite-sequencing reads.40691759 · Nikaein, Hassan, Sharifi-Zarchi, Ali, Afzal, Afsoon et al.2025 · 0 citationsBMC bioinformatics. 2025;26(1):188
Pan-cancer analysis of microRNA expression profiles highlights microRNAs enriched in normal body cells as effective suppressors of multiple tumor types: A study based on TCGA database.35476804 · Moradi, Sharif, Kamal, Aryan, Aboulkheyr Es, Hamidreza et al.2022 · 23 citationsPloS one. 2022;17(4):e0267291
SARS-CoV-2 orthologs of pathogenesis-involved small viral RNAs of SARS-CoV2007.05859v2 · Ali Ebrahimpour Boroojeny, Hamidreza Chitsaz2020 · 1 citationarXiv
PyGTED: Python Application for Computing Graph Traversal Edit Distance.32160033 · Ebrahimpour Boroojeny, Ali, Shrestha, Akash, Sharifi-Zarchi, Ali et al.2021 · 2 citationsJournal of computational biology : a journal of computational molecular cell biology. 2020;27(3):436-439
Graph Traversal Edit Distance and Extensions.32058803 · Ebrahimpour Boroojeny, Ali, Shrestha, Akash, Sharifi-Zarchi, Ali et al.2021 · 5 citationsJournal of computational biology : a journal of computational molecular cell biology. 2020;27(3):317-329
Enrichment of ovine gonadotropes via adenovirus gene targeting enhances assessment of transcriptional changes in response to estradiol-17 beta†.31504222 · Murtazina, Dilyara A, Arreguin-Arevalo, Jesus Alejandro, Cantlon, Jeremy D et al.2021 · 3 citationsBiology of reproduction. 2020;102(1):156-169
DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome.31712594 · Azarkhalili, Behrooz, Saberi, Ali, Chitsaz, Hamidreza et al.2020 · 43 citationsScientific reports. 2019;9(1):16526
BPPart and BPMax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model1904.01235v2 · Ali Ebrahimpour-Boroojeny, Sanjay Rajopadhye, Hamidreza Chitsaz2019 · 2 citationsarXiv
Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks.30787315 · Abdolhosseini, Farzad, Azarkhalili, Behrooz, Maazallahi, Abbas et al.2020 · 23 citationsScientific reports. 2019;9(1):2342
Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians.30181897 · An, Yang, Kawaguchi, Akane, Zhao, Chen et al.2022 · 40 citationsZoological letters. 2018;4:24
DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism.29233090 · Sharifi-Zarchi, Ali, Gerovska, Daniela, Adachi, Kenjiro et al.2018 · 127 citationsBMC genomics. 2017;18(1):964
Scalable Nonlinear AUC Maximization Methods1710.00760v4 · Majdi Khalid, Indrakshi Ray, Hamidreza Chitsaz2017 · 7 citationsarXiv
Genomewide Analysis of Clp1 Function in Transcription in Budding Yeast.28761171 · Al-Husini, Nadra, Sharifi, Ali, Mousavi, Seyed Ahmad et al.2019 · 5 citationsScientific reports. 2017;7(1):6894
Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase.28623339 · Karamzadeh, Razieh, Karimi-Jafari, Mohammad Hossein, Sharifi-Zarchi, Ali et al.2019 · 43 citationsScientific reports. 2017;7(1):3666
SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature.28388928 · Bokharaeian, Behrouz, Diaz, Alberto, Taghizadeh, Nasrin et al.2017 · 25 citationsJournal of biomedical semantics. 2017;8(1):14
Proceedings of the 1st International Workshop on Robot Learning and Planning (RLP 2016)1610.02573v1 · Nancy Amato, Charles Anderson, Gregory Chirikjian et al.2016 · 1 citationarXiv
Enhancing Extraction of Drug-Drug Interaction from Literature Using Neutral Candidates, Negation, and Clause Dependency.27695078 · Bokharaeian, Behrouz, Diaz, Alberto, Chitsaz, Hamidreza2017 · 30 citationsPloS one. 2016;11(10):e0163480
Confidence-Weighted Bipartite Ranking1607.00847v9 · Majdi Khalid, Indrakshi Ray, Hamidreza Chitsaz2016 · 1 citationarXiv
Efficient Synergistic Single-Cell Genome Assembly.27243002 · Movahedi, Narjes S, Embree, Mallory, Nagarajan, Harish et al.2016 · 5 citationsFrontiers in bioengineering and biotechnology. 2016;4:42
Increased robustness of early embryogenesis through collective decision-making by key transcription factors.26033487 · Sharifi-Zarchi, Ali, Totonchi, Mehdi, Khaloughi, Keynoush et al.2016 · 10 citationsBMC systems biology. 2015;9:23
Exact learning of RNA energy parameters from structure.25756654 · Chitsaz, Hamidreza, Aminisharifabad, Mohammad2016 · 9 citationsJournal of computational biology : a journal of computational molecular cell biology. 2015;22(6):463-73
NUROA: A Numerical Roadmap Algorithm1403.5384v2 · Reza Iraji, Hamidreza Chitsaz2014 · 3 citationsarXiv
ARYANA: Aligning Reads by Yet Another Approach.25252881 · Gholami, Milad, Arbabi, Aryan, Sharifi-Zarchi, Ali et al.2014 · 1 citationBMC bioinformatics. 2014;15 Suppl 9:S12
HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly.25558875 · Shariat, Basir, Movahedi, Narjes Sadat, Chitsaz, Hamidreza et al.2015 · 13 citationsBMC genomics. 2014;15 Suppl 10:S9
Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community.24152715 · Embree, Mallory, Nagarajan, Harish, Movahedi, Narjes et al.2014 · 127 citationsThe ISME journal. 2014;8(4):757-67
Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities.23918251 · Taghavi, Zeinab, Movahedi, Narjes S, Draghici, Sorin et al.2014 · 7 citationsBioinformatics (Oxford, England). 2013;29(19):2395-401
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.23870653 · Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton et al.2014 · 671 citationsGigaScience. 2013;2(1):10
The RNA Newton polytope and learnability of energy parameters.23812998 · Forouzmand, Elmirasadat, Chitsaz, Hamidreza2013 · 3 citationsBioinformatics (Oxford, England). 2013;29(13):i300-7
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.23754396 · McLean, Jeffrey S, Lombardo, Mary-Jane, Badger, Jonathan H et al.2013 · 171 citationsProceedings of the National Academy of Sciences of the United States of America. 2013;110(26):E2390-9
An efficient algorithm for upper bound on the partition function of nucleic acids.23829650 · Chitsaz, Hamidreza, Forouzmand, Elmirasadat, Haffari, Gholamreza2014 · 2 citationsJournal of computational biology : a journal of computational molecular cell biology. 2013;20(7):486-94
On Time-optimal Trajectories for a Car-like Robot with One Trailer1301.6662v1 · Hamidreza Chitsaz2013 · 7 citationsarXiv
SEQuel: improving the accuracy of genome assemblies.22689760 · Ronen, Roy, Boucher, Christina, Chitsaz, Hamidreza et al.2013 · 64 citationsBioinformatics (Oxford, England). 2012;28(12):i188-96
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.21926975 · Chitsaz, Hamidreza, Yee-Greenbaum, Joyclyn L, Tesler, Glenn et al.2012 · 236 citationsNature biotechnology. 2011;29(10):915-21
Prediction of RNA-RNA interaction structure by centroids in the Boltzmann ensemble1002.1736v1 · Hamidreza Chitsaz2010 · 1 citationarXiv
A partition function algorithm for interacting nucleic acid strands.19478011 · Chitsaz, Hamidreza, Salari, Raheleh, Sahinalp, S Cenk et al.2009 · 102 citationsBioinformatics (Oxford, England). 2009;25(12):i365-73
Career total: 61 works. 35 are in this corpus.
Profile built from the corpus for this byline.
Author records are still filling in while the Hub is in alpha. If this is your page, you'll be able to claim it soon. Spot a mistake? Tell us.